hmmm I remember doing this one different.... I had my entire fleet gathered at one wormhole (not my home planet one). and each time I send in one starship.... and either have it killed or send it back to my main fleet right away... and every time about a 100 enemy ships came through and my fleet + turrets could easily destroy them all. I did this 3 or 4 times till there were no more ships left between the wormhole and the warp gate. he didn't attack my homeplanet other than the usual waves. And after I destroyed their warp gate I pretty much left the remaining 500 enemy ships on that planet alone. I have been wiped out once when attacking their home planet but I don't recall having much trouble with that warp gate raid

Looking back at this now, I think if I faced a similar situation I'd probably try to exterminate the guards near the wormhole first, taking advantage of the others not "waking up" until you actually approach their guard post, and then send in Raid starships for the warp gate (taking care they don't fly too close to any other concentrations of enemies). That way, you probably only have to deal with 100-200 ships at a time, which is a bit rough when you're outmarked but manageable. You could also try to lure the first clump of guards through the wormhole intentionally so your turrets could cut them up.

If I remember right, at the time I didn't realize you could build force fields to block the wormholes the AI needs to pass to get to your homeworld. You can, and I would do that, usually putting the command center underneath it to save on the unit cap. Logistics and military command stations can also add a lot to your defense. That choice is discussed really well in this thread: http://www.arcengames.com/forums/index.php/topic,8169.0.html